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  1. Article ; Online: Use of "Coldspot" Regions in Variant Classification.

    Harrison, Steven M / Funke, Birgit

    Clinical chemistry

    2020  Volume 66, Issue 10, Page(s) 1263–1265

    Language English
    Publishing date 2020-10-01
    Publishing country England
    Document type Journal Article ; Comment
    ZDB-ID 80102-1
    ISSN 1530-8561 ; 0009-9147
    ISSN (online) 1530-8561
    ISSN 0009-9147
    DOI 10.1093/clinchem/hvaa133
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  2. Article ; Online: Development of twenty-one novel microsatellite loci for Gila topminnow, Poeciliopsis occidentalis occidentalis.

    Mussmann, Steven M / Harrison, Alexis S / Wilson, Wade D

    Molecular biology reports

    2023  Volume 50, Issue 5, Page(s) 4743–4751

    Abstract: Background: Gila topminnow (Poeciliopsis occidentalis occidentalis) was once highly abundant throughout the Lower Colorado River Basin of the southwestern United States. However, this Sonoran Desert endemic suffered extreme population declines over the ... ...

    Abstract Background: Gila topminnow (Poeciliopsis occidentalis occidentalis) was once highly abundant throughout the Lower Colorado River Basin of the southwestern United States. However, this Sonoran Desert endemic suffered extreme population declines over the past century because of habitat degradation and nonnative species introductions. Much of the prior conservation genetic work conducted on the species relied upon a small number of microsatellite loci; many exhibiting low variability in extant populations. Consequently, there was a need for additional microsatellite loci to provide high-resolution delimitation of populations for conservation purposes.
    Methods and results: Paired-end Illumina sequencing was utilized to screen the Gila topminnow genome for novel microsatellite loci. We identified 21 novel loci that exhibited no deviations from expectations of genetic equilibrium, and cross-amplified in Yaqui topminnow (P. o. sonoriensis). These loci were amplified from 401 samples representing eight populations of Gila topminnow and Yaqui topminnow. Although diversity was low for all populations (observed heterozygosity = 0.12 to 0.45), these novel markers provided ample power to identify population of origin for each individual in Bayesian assignment tests.
    Conclusions: This novel set of microsatellite loci provide a useful genetic tool to assess population genetic parameters of the endangered Gila topminnow and delineate populations for identifying conservation priorities. The cross-amplification of these loci in Yaqui topminnow shows promise for application to other Poeciliopsis species of Mexico and Central America.
    MeSH term(s) Animals ; Fundulidae ; Bayes Theorem ; Gene Frequency ; Heterozygote ; Microsatellite Repeats/genetics ; Genetics, Population ; Genetic Loci/genetics
    Language English
    Publishing date 2023-03-20
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 186544-4
    ISSN 1573-4978 ; 0301-4851
    ISSN (online) 1573-4978
    ISSN 0301-4851
    DOI 10.1007/s11033-023-08376-7
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  3. Article ; Online: Incidence and transmission associated with respiratory viruses in an acute care facility: An observational study.

    Valek, Abby L / Srinivasa, Vatsala Rangachar / Ayres, Ashley M / Cheung, Steven / Harrison, Lee H / Snyder, Graham M

    Infection control and hospital epidemiology

    2024  , Page(s) 1–3

    Abstract: We estimated the extent of respiratory virus transmission over three pre-COVID-19 seasons. Of 16,273 assays, 22.9% (3,726) detected ≥1 respiratory virus. The frequency of putatively hospital-acquired infection ranged from 6.9% (influenza A/B) to 24.7% ( ... ...

    Abstract We estimated the extent of respiratory virus transmission over three pre-COVID-19 seasons. Of 16,273 assays, 22.9% (3,726) detected ≥1 respiratory virus. The frequency of putatively hospital-acquired infection ranged from 6.9% (influenza A/B) to 24.7% (adenovirus). The 176 clusters were most commonly associated with rhinovirus/enterovirus (70) and influenza A/B (62).
    Language English
    Publishing date 2024-02-14
    Publishing country United States
    Document type Journal Article
    ZDB-ID 639378-0
    ISSN 1559-6834 ; 0195-9417 ; 0899-823X
    ISSN (online) 1559-6834
    ISSN 0195-9417 ; 0899-823X
    DOI 10.1017/ice.2024.25
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  4. Article ; Online: Is 'likely pathogenic' really 90% likely? Reclassification data in ClinVar.

    Harrison, Steven M / Rehm, Heidi L

    Genome medicine

    2019  Volume 11, Issue 1, Page(s) 72

    Abstract: In 2015, professional guidelines defined the term 'likely pathogenic' to mean with a 90% chance of pathogenicity. To determine whether current practice reflects this definition, ClinVar classifications were tracked from 2016 to 2019. During that period, ... ...

    Abstract In 2015, professional guidelines defined the term 'likely pathogenic' to mean with a 90% chance of pathogenicity. To determine whether current practice reflects this definition, ClinVar classifications were tracked from 2016 to 2019. During that period, between 83.8 and 99.1% of likely pathogenic classifications were reclassified as pathogenic, depending on whether LP to VUS reclassifications are included and on how these classifications are categorized.
    MeSH term(s) Genetic Association Studies/methods ; Genetic Predisposition to Disease ; Genetic Testing/methods ; Humans ; Practice Guidelines as Topic
    Language English
    Publishing date 2019-11-21
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 2484394-5
    ISSN 1756-994X ; 1756-994X
    ISSN (online) 1756-994X
    ISSN 1756-994X
    DOI 10.1186/s13073-019-0688-9
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  5. Article ; Online: The ACMG/AMP reputable source criteria for the interpretation of sequence variants.

    Biesecker, Leslie G / Harrison, Steven M

    Genetics in medicine : official journal of the American College of Medical Genetics

    2018  Volume 20, Issue 12, Page(s) 1687–1688

    MeSH term(s) Adenosine Monophosphate ; Consensus ; Genetics, Medical ; Genomics ; Pathology, Molecular ; United States
    Chemical Substances Adenosine Monophosphate (415SHH325A)
    Language English
    Publishing date 2018-03-13
    Publishing country United States
    Document type Letter ; Comment
    ZDB-ID 1455352-1
    ISSN 1530-0366 ; 1098-3600
    ISSN (online) 1530-0366
    ISSN 1098-3600
    DOI 10.1038/gim.2018.42
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  6. Article ; Online: Correspondence on "The role of clinical response to treatment in determining pathogenicity of genomic variants" by Shen et al.

    Biesecker, Leslie G / Harrison, Steven M / Rehm, Heidi L

    Genetics in medicine : official journal of the American College of Medical Genetics

    2020  Volume 23, Issue 3, Page(s) 586

    MeSH term(s) Consensus ; Genetics, Medical ; Genomics ; Humans ; Pathology, Molecular ; United States ; Virulence
    Language English
    Publishing date 2020-11-06
    Publishing country United States
    Document type Letter ; Comment
    ZDB-ID 1455352-1
    ISSN 1530-0366 ; 1098-3600
    ISSN (online) 1530-0366
    ISSN 1098-3600
    DOI 10.1038/s41436-020-01032-6
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  7. Article ; Online: Clinical interpretation of KCNH2 variants using a robust PS3/BS3 functional patch-clamp assay.

    Thomson, Kate L / Jiang, Connie / Richardson, Ebony / Westphal, Dominik S / Burkard, Tobias / Wolf, Cordula M / Vatta, Matteo / Harrison, Steven M / Ingles, Jodie / Bezzina, Connie R / Kroncke, Brett M / Vandenberg, Jamie I / Ng, Chai-Ann

    HGG advances

    2024  Volume 5, Issue 2, Page(s) 100270

    Abstract: Long QT syndrome (LQTS), caused by the dysfunction of cardiac ion channels, increases the risk of sudden death in otherwise healthy young people. For many variants in LQTS genes, there is insufficient evidence to make a definitive genetic diagnosis. We ... ...

    Abstract Long QT syndrome (LQTS), caused by the dysfunction of cardiac ion channels, increases the risk of sudden death in otherwise healthy young people. For many variants in LQTS genes, there is insufficient evidence to make a definitive genetic diagnosis. We have established a robust functional patch-clamp assay to facilitate classification of missense variants in KCNH2, one of the key LQTS genes. A curated set of 30 benign and 30 pathogenic missense variants were used to establish the range of normal and abnormal function. The extent to which variants reduced protein function was quantified using Z scores, the number of standard deviations from the mean of the normalized current density of the set of benign variant controls. A Z score of -2 defined the threshold for abnormal loss of function, which corresponds to 55% wild-type function. More extreme Z scores were observed for variants with a greater loss-of-function effect. We propose that the Z score for each variant can be used to inform the application and weighting of abnormal and normal functional evidence criteria (PS3 and BS3) within the American College of Medical Genetics and Genomics variant classification framework. The validity of this approach was demonstrated using a series of 18 KCNH2 missense variants detected in a childhood onset LQTS cohort, where the level of function assessed using our assay correlated to the Schwartz score (a scoring system used to quantify the probability of a clinical diagnosis of LQTS) and the length of the corrected QT (QTc) interval.
    MeSH term(s) Child ; Humans ; Death, Sudden ; ERG1 Potassium Channel/genetics ; Heart ; Long QT Syndrome/diagnosis ; Mutation, Missense
    Chemical Substances ERG1 Potassium Channel ; KCNH2 protein, human
    Language English
    Publishing date 2024-01-14
    Publishing country United States
    Document type Journal Article
    ISSN 2666-2477
    ISSN (online) 2666-2477
    DOI 10.1016/j.xhgg.2024.100270
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  8. Article ; Online: No mark is an island: Precision and category repulsion biases in data reproductions.

    McColeman, Caitlyn M / Harrison, Lane / Feng, Mi / Franconeri, Steven

    IEEE transactions on visualization and computer graphics

    2021  Volume 27, Issue 2, Page(s) 1063–1072

    Abstract: Data visualization is powerful in large part because it facilitates visual extraction of values. Yet, existing measures of perceptual precision for data channels (e.g., position, length, orientation, etc.) are based largely on verbal reports of ratio ... ...

    Abstract Data visualization is powerful in large part because it facilitates visual extraction of values. Yet, existing measures of perceptual precision for data channels (e.g., position, length, orientation, etc.) are based largely on verbal reports of ratio judgments between two values (e.g., [7]). Verbal report conflates multiple sources of error beyond actual visual precision, introducing a ratio computation between these values and a requirement to translate that ratio to a verbal number. Here we observe raw measures of precision by eliminating both ratio computations and verbal reports; we simply ask participants to reproduce marks (a single bar or dot) to match a previously seen one. We manipulated whether the mark was initially presented (and later drawn) alone, paired with a reference (e.g. a second '100%' bar also present at test, or a y-axis for the dot), or integrated with the reference (merging that reference bar into a stacked bar graph, or placing the dot directly on the axis). Reproductions of smaller values were overestimated, and larger values were underestimated, suggesting systematic memory biases. Average reproduction error was around 10% of the actual value, regardless of whether the reproduction was done on a common baseline with the original. In the reference and (especially) the integrated conditions, responses were repulsed from an implicit midpoint of the reference mark, such that values above 50% were overestimated, and values below 50% were underestimated. This reproduction paradigm may serve within a new suite of more fundamental measures of the precision of graphical perception.
    Language English
    Publishing date 2021-01-28
    Publishing country United States
    Document type Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
    ISSN 1941-0506
    ISSN (online) 1941-0506
    DOI 10.1109/TVCG.2020.3030345
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  9. Article ; Online: The influence of manure-based organic fertilisers on the oviposition behaviour of Anopheles arabiensis

    Hardy, Harrison / Harte, Steven J. / Hopkins, Richard J. / Mnyone, Ladslaus / Hawkes, Frances M.

    Acta Tropica. 2023 Aug., v. 244 p.106954-

    2023  

    Abstract: The rice agroecosystem provides suitable breeding habitat for many malaria vector species, and rice-adjacent communities are consequently exposed to a greater malaria transmission risk than non-rice-associated communities. As part of efforts to expand ... ...

    Abstract The rice agroecosystem provides suitable breeding habitat for many malaria vector species, and rice-adjacent communities are consequently exposed to a greater malaria transmission risk than non-rice-associated communities. As part of efforts to expand rice production in Africa, sustainable and climate-adapted practices such as the System of Rice Intensification (SRI) are being promoted. SRI encourages the use of organic fertilisers (OFs) such as cow and chicken dung, as opposed to inorganic industrially produced fertilisers, due to their lower resource cost, apparent benefit to the rice agroecosystem and as a means to reduce the greenhouse gas emissions associated with the production of industrial fertilisers. However, the impact of OFs on mosquito fauna is not well documented and may have knock-on consequences on malaria transmission risk. Here, we demonstrate, using dual choice egg count assays, that both cow and chicken dung modulate the oviposition behaviour of Anopheles arabiensis, a major malaria vector in Sub-Saharan Africa. A significantly reduced proportion of eggs were laid in water treated with either cow or chicken dung compared to untreated water, with higher dung concentrations resulting in further reduced proportions. When presented in competition, significantly fewer eggs were laid in water treated with chicken dung than with cow dung. Moreover, there was no evidence of egg retention in any experiment, including in no-choice experiments where only dung-containing dishes were available. These results suggest both cow and chicken dung may act as oviposition deterrents to malaria vector species and that the application of manure-based OFs in rice agriculture may modulate the oviposition behaviour of An. gambiae s.l. within agroecosystems. Quantification of the ammonia present in dung-infused water showed higher concentrations were present in the chicken dung infusion, which may be one contributing factor to the difference in observed deterrence between the two dung types. Deterrence of mosquito oviposition in OF-treated farms may potentially affect the overall production of malaria vectors within rice fields and their contribution to local malaria transmission.
    Keywords Anopheles arabiensis ; agroecosystems ; ammonia ; chickens ; cow manure ; cows ; eggs ; fauna ; feces ; greenhouse gases ; habitats ; malaria ; mosquito vectors ; oviposition ; rice ; risk ; Sub-Saharan Africa ; Organic fertilisers ; Rice cultivation ; Malaria vectors
    Language English
    Dates of publication 2023-08
    Publishing place Elsevier B.V.
    Document type Article ; Online
    Note Pre-press version
    ZDB-ID 210415-5
    ISSN 1873-6254 ; 0001-706X
    ISSN (online) 1873-6254
    ISSN 0001-706X
    DOI 10.1016/j.actatropica.2023.106954
    Database NAL-Catalogue (AGRICOLA)

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    Z 52/75: Show issues

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  10. Article ; Online: Zebra sign in cerebellar haemorrhage after craniotomy.

    Nigam, Minali / Harrison, Daniel Steven / Bhattacharyya, Shamik

    BMJ case reports

    2023  Volume 16, Issue 12

    MeSH term(s) Humans ; Cerebral Hemorrhage/diagnostic imaging ; Cerebral Hemorrhage/etiology ; Craniotomy/adverse effects ; Cerebellar Diseases/diagnostic imaging ; Cerebellar Diseases/etiology ; Cerebellum/diagnostic imaging ; Cerebellum/surgery
    Language English
    Publishing date 2023-12-11
    Publishing country England
    Document type Case Reports ; Journal Article
    ISSN 1757-790X
    ISSN (online) 1757-790X
    DOI 10.1136/bcr-2023-256736
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